Department of Biology, University of Maryland, 1210 Biology / Psychology Bldg #144, College Park, MD, 20742, USA.
BMC Genomics. 2018 Dec 18;19(1):945. doi: 10.1186/s12864-018-5328-z.
Dissecting the genetic basis of phenotypic diversity is one of the fundamental goals in evolutionary biology. Despite growing evidence for gene expression divergence being responsible for the evolution of complex traits, knowledge about the proximate genetic causes underlying these traits is still limited. African cichlids have diverse visual systems, with different species expressing different combinations of seven cone opsin genes. Using opsin expression variation in African cichlids as a model for gene expression evolution, this study aims to investigate the genetic architecture of opsin expression divergence in this group.
Results from a genome-wide linkage mapping on the F progeny of an intergeneric cross, between two species with differential opsin expression show that opsins in Lake Malawi cichlids are controlled by multiple quantitative trait loci (QTLs). Most of these QTLs are located in trans to the opsins except for one cis-QTL for SWS1 on LG17. A closer look at this major QTL revealed the presence of a 691 bp deletion in the promoter of the SWS1 opsin (located 751 bp upstream of the start site) that is associated with a decrease in its expression. Phylogenetic footprinting indicates that the region spanning the deletion harbors a microRNA miR-729 and a conserved non-coding element (CNE) that also occurs in zebrafish and other teleosts. This suggests that the deletion might contain ancestrally preserved regulators that have been tuned for SWS1 gene expression in Lake Malawi. While this deletion is not common, it does occur in several other species within the lake.
Differential expression of cichlid opsins is associated with multiple overlapping QTL, with all but one in trans to the opsins they regulate. The one cis-acting factor is a deletion in the promoter of the SWS1 opsin, suggesting that ancestral polymorphic deletions may contribute to cichlid's visual diversity. In addition to expanding our understanding of the molecular landscape of opsin expression in African cichlids, this study sheds light on the molecular mechanisms underlying phenotypic variation in natural populations.
剖析表型多样性的遗传基础是进化生物学的基本目标之一。尽管越来越多的证据表明基因表达的差异是复杂特征进化的原因，但对于这些特征的潜在遗传原因的了解仍然有限。非洲丽鱼科具有多样化的视觉系统，不同物种表达七种视蛋白基因的不同组合。本研究以非洲丽鱼科的视蛋白表达变异为模型，旨在研究该类群中视蛋白表达差异的遗传结构。
对两个具有不同视蛋白表达的物种的属间杂交的 F 代进行全基因组连锁图谱分析的结果表明，马拉维湖丽鱼的视蛋白受多个数量性状基因座（QTL）控制。这些 QTL 中的大多数位于视蛋白的转位上，除了位于 LG17 上的 SWS1 顺式-QTL 之外。对这个主要 QTL 的进一步研究揭示了 SWS1 视蛋白启动子中存在 691bp 的缺失（位于起始位点上游 751bp 处），这与它的表达减少有关。系统发育足迹分析表明，跨越缺失的区域包含一个 microRNA miR-729 和一个保守的非编码元件（CNE），该元件也存在于斑马鱼和其他硬骨鱼中。这表明缺失可能包含了祖先保留的调控因子，这些调控因子已经针对马拉维湖中 SWS1 基因的表达进行了调整。虽然这种缺失并不常见，但它确实在湖中存在于其他几个物种中。
丽鱼科视蛋白的差异表达与多个重叠的 QTL 相关，除了一个顺式作用因子之外，其余的都在它们调节的视蛋白的转位上。这个顺式作用因子是 SWS1 视蛋白启动子中的缺失，这表明祖先多态性缺失可能有助于丽鱼的视觉多样性。除了扩大我们对非洲丽鱼科视蛋白表达的分子景观的理解外，本研究还揭示了自然种群中表型变异的分子机制。
